This class implements generic methods for sequences with residue-based meta information. Meta sequences with meta data are Bio::LocatableSeq objects with additional methods to store that meta information. See Bio::LocatableSeq and Bio::Seq::MetaI.

The meta information in this class can be a string of variable length and can be a complex structure. Blank values are undef or zero.

Application specific implementations should inherit from this class to override and add to these methods.

This class can be used for storing sequence quality values but Bio::Seq::Quality has named methods that make it easier.

This Bio::Seq::MetaI implementation inherits from Bio::LocatableSeq, which itself inherits from Bio::PrimarySeq. It is not a Bio::SeqI, so bless-ing objects of this class into a Bio::SeqI or vice versa and will not work as expected (see bug 2262). This may be addressed in a future refactor of Bio::LocatableSeq.

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Title : meta
Usage : $meta_values = $obj->meta($values_string);
Function:
Get and set method for the meta data starting from residue
position one. Since it is dependent on the length of the
sequence, it needs to be manipulated after the sequence.
The length of the returned value always matches the length
of the sequence.
Returns : reference to an array of meta data
Args : new value, string or array ref, optional

Title : named_meta()
Usage : $meta_values = $obj->named_meta($name, $values_arrayref);
Function: A more general version of meta(). Each meta data set needs
to be named. See also L<meta_names>.
Returns : reference to an array of meta data
Args : scalar, name of the meta data set
new value, string or array ref, optional

Title : _test_gap_positions
Usage : $meta_values = $obj->_test_gap_positions($name);
Function: Internal test for correct position of gap characters.
Gap being only '-' this time.
This method is called from named_meta() when setting meta
data but only if verbose is positive as this can be an
expensive process on very long sequences. Set verbose(1) to
see warnings when gaps do not align in sequence and meta
data and turn them into errors by setting verbose(2).
Returns : true on success, prints warnings
Args : none

Title : named_meta_text()
Usage : $meta_values = $obj->named_meta_text($name, $values_arrayref);
Function: Variant of named_meta() guarantied to return a textual
representation of the named meta data.
For details, see L<meta>.
Returns : a string
Args : scalar, name of the meta data set
new value, string or array ref, optional

Title : submeta
Usage : $subset_of_meta_values = $obj->submeta(10, 20, $value_string);
$subset_of_meta_values = $obj->submeta(10, undef, $value_string);
Function:
Get and set method for meta data for subsequences.
Numbering starts from 1 and the number is inclusive, ie 1-2
are the first two residue of the sequence. Start cannot be
larger than end but can be equal.
If the second argument is missing the returned values
should extend to the end of the sequence.
The return value may be a string or an array reference,
depending on the implementation. If in doubt, use
submeta_text() which is a variant guarantied to return a
string. See L<submeta_text>.
Returns : A reference to an array or a string
Args : integer, start position
integer, end position, optional when a third argument present
new value, string or array ref, optional

Title : named_submeta
Usage : $subset_of_meta_values = $obj->named_submeta($name, 10, 20, $value_string);
$subset_of_meta_values = $obj->named_submeta($name, 10);
Function: Variant of submeta() guarantied to return a textual
representation of meta data. For details, see L<meta>.
Returns : A reference to an array or a string
Args : scalar, name of the meta data set
integer, start position
integer, end position, optional when a third argument present (can be undef)
new value, string or array ref, optional

Title : meta_names
Usage : @meta_names = $obj->meta_names()
Function: Retrieves an array of meta data set names. The default
(unnamed) set name is guarantied to be the first name if it
contains any data.
Returns : an array of names
Args : none

Title : is_flush
Usage : $is_flush = $obj->is_flush()
or $is_flush = $obj->is_flush($my_meta_name)
Function: Boolean to tell if all meta values are in
flush with the sequence length.
Returns true if force_flush() is set
Set verbosity to a positive value to see failed meta sets
Returns : boolean 1 or 0
Args : optional name of the meta set

Title : revcom
Usage : $newseq = $seq->revcom();
Function: Produces a new Bio::Seq::MetaI implementing object where
the order of residues and their meta information is reversed.
Returns : A new (fresh) Bio::Seq::Meta object
Args : none
Throws : if the object returns false on is_flush()

Title : trunc
Usage : $subseq = $seq->trunc(10,100);
Function: Provides a truncation of a sequence together with meta data
Returns : a fresh Bio::Seq::Meta implementing object
Args : Two integers denoting first and last residue of the sub-sequence.